Pub Date : 2023-11-08DOI: 10.1109/TMBMC.2023.3329801
Mustafa Can Gursoy;Urbashi Mitra
Diffusion-based molecular communications (DBMC) systems rely on diffusive propagation of molecules to convey information. In a DBMC system, as each emitted molecule experiences a stochastic delay, pulse shaping is crucial for a DBMC system’s reliability and overall performance. To this end, acknowledging the inherent resource-limited nature of a DBMC system, a novel framework to model and optimize a DBMC transmitter is introduced in this paper. Leveraging tools from wireless packet scheduling theory, the DBMC pulse shaping problem is formulated as an energy-constrained resource allocation problem. Through the developed framework, it is shown that the provably optimal pulse shape that minimizes the error probability is the delayed-spike pulse, where the incurred delay is a decreasing function of the available energy budget. The framework is then extended to both absorbing and passive/observing receiver structures, as well as systems where molecules can degrade in the transmitter body prior to release. Numerical results corroborate the developed analysis, and show that the delayed-spike outperforms conventional, non-zero-width pulse shapes in terms of error performance.
{"title":"Scheduling-Based Transmit Signal Shaping in Energy-Constrained Molecular Communications","authors":"Mustafa Can Gursoy;Urbashi Mitra","doi":"10.1109/TMBMC.2023.3329801","DOIUrl":"10.1109/TMBMC.2023.3329801","url":null,"abstract":"Diffusion-based molecular communications (DBMC) systems rely on diffusive propagation of molecules to convey information. In a DBMC system, as each emitted molecule experiences a stochastic delay, pulse shaping is crucial for a DBMC system’s reliability and overall performance. To this end, acknowledging the inherent resource-limited nature of a DBMC system, a novel framework to model and optimize a DBMC transmitter is introduced in this paper. Leveraging tools from wireless packet scheduling theory, the DBMC pulse shaping problem is formulated as an energy-constrained resource allocation problem. Through the developed framework, it is shown that the provably optimal pulse shape that minimizes the error probability is the delayed-spike pulse, where the incurred delay is a decreasing function of the available energy budget. The framework is then extended to both absorbing and passive/observing receiver structures, as well as systems where molecules can degrade in the transmitter body prior to release. Numerical results corroborate the developed analysis, and show that the delayed-spike outperforms conventional, non-zero-width pulse shapes in terms of error performance.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"447-460"},"PeriodicalIF":2.2,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135508660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In the most severe COVID-19 cases, often the cytokine molecules produced by the immune system to fight off coronavirus infection become hyperactive. This leads to “cytokine storm”, which is a serious adverse medical condition causing multiple organ failures. In this work, we propose a system model that captures the transmission of cytokines from the alveoli, the propagation via the vascular channel, and the reception in the blood vessel wall. We analyze the impact of different diseases on induced cytokine storm. The proposed analytical model helps observe the behavior of cytokine storm in different medical conditions. We perform particle-based simulations to analyze the proposed end-to-end channel model describing the cytokine storm in terms of gain and delay, which is inspired from the existing molecular communication channel models from literature. We observe that the channel gain mostly remains unaffected for upto three times increase in the channel length, while, with four times increase, the gain increases upto 16% at 1000 rad/s frequency. We analyze the channel response to the different stimuli of interactions between the cytokines and their varying release rates. We evaluate the cytokine signal at the receiver and observe that lesser diffusion leads to higher cytokine concentration at the receiver.
{"title":"Channel Characterization of Molecular Communications for Cytokine Storm in COVID-19 Patients","authors":"Saswati Pal;Sudip Misra;Nabiul Islam;Sasitharan Balasubramaniam","doi":"10.1109/TMBMC.2023.3327869","DOIUrl":"10.1109/TMBMC.2023.3327869","url":null,"abstract":"In the most severe COVID-19 cases, often the cytokine molecules produced by the immune system to fight off coronavirus infection become hyperactive. This leads to “cytokine storm”, which is a serious adverse medical condition causing multiple organ failures. In this work, we propose a system model that captures the transmission of cytokines from the alveoli, the propagation via the vascular channel, and the reception in the blood vessel wall. We analyze the impact of different diseases on induced cytokine storm. The proposed analytical model helps observe the behavior of cytokine storm in different medical conditions. We perform particle-based simulations to analyze the proposed end-to-end channel model describing the cytokine storm in terms of gain and delay, which is inspired from the existing molecular communication channel models from literature. We observe that the channel gain mostly remains unaffected for upto three times increase in the channel length, while, with four times increase, the gain increases upto 16% at 1000 rad/s frequency. We analyze the channel response to the different stimuli of interactions between the cytokines and their varying release rates. We evaluate the cytokine signal at the receiver and observe that lesser diffusion leads to higher cytokine concentration at the receiver.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"425-434"},"PeriodicalIF":2.2,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135212692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-24DOI: 10.1109/TMBMC.2023.3327302
Hadeel Elayan;Andrew W. Eckford;Raviraj S. Adve
Folding of proteins into their correct native structure is key to their function. Simultaneously, the intricate interplay between cell movement and protein conformation highlights the complex nature of cellular processes. In this work, we demonstrate the impact of Terahertz (THz) signaling on controlling protein conformational changes in a random medium. Our system of interest consists of a communication link that involves a nanoantenna transmitter, a protein receiver, and a channel composed of moving red blood cells. Due to the system dynamics, we investigate the influence of both the fast and slow channel variations on protein folding. Specifically, we analyze the system’s selectivity to asses the effectiveness of the induced THz interaction in targeting a specific group of proteins under fading conditions. By optimizing the selectivity metric with respect to the nanoantenna power and frequency, it is possible to enhance the controllability of protein interactions. Our probabilistic analysis provides a new perspective regarding electromagnetically triggered protein molecules, their micro-environment and their interaction with surrounding particles. It helps elucidate how external conditions impact the protein folding kinetics and pathways. This results in not only understanding the mechanisms underlying THz-induced protein interactions but also engineering these still-emerging tools.
{"title":"Terahertz Induced Protein Interactions in a Random Medium","authors":"Hadeel Elayan;Andrew W. Eckford;Raviraj S. Adve","doi":"10.1109/TMBMC.2023.3327302","DOIUrl":"10.1109/TMBMC.2023.3327302","url":null,"abstract":"Folding of proteins into their correct native structure is key to their function. Simultaneously, the intricate interplay between cell movement and protein conformation highlights the complex nature of cellular processes. In this work, we demonstrate the impact of Terahertz (THz) signaling on controlling protein conformational changes in a random medium. Our system of interest consists of a communication link that involves a nanoantenna transmitter, a protein receiver, and a channel composed of moving red blood cells. Due to the system dynamics, we investigate the influence of both the fast and slow channel variations on protein folding. Specifically, we analyze the system’s selectivity to asses the effectiveness of the induced THz interaction in targeting a specific group of proteins under fading conditions. By optimizing the selectivity metric with respect to the nanoantenna power and frequency, it is possible to enhance the controllability of protein interactions. Our probabilistic analysis provides a new perspective regarding electromagnetically triggered protein molecules, their micro-environment and their interaction with surrounding particles. It helps elucidate how external conditions impact the protein folding kinetics and pathways. This results in not only understanding the mechanisms underlying THz-induced protein interactions but also engineering these still-emerging tools.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"435-446"},"PeriodicalIF":2.2,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135158256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-19DOI: 10.1109/TMBMC.2023.3325405
Max Bartunik;Janina Teller;Georg Fischer;Jens Kirchner
Testbeds play an essential role in the development of real-life molecular communication applications and experimental validation of communication channel models. Although some testbed concepts have been published in recent years, very few setups are inherently suitable for biomedical applications. Furthermore, systematic experimental data of a wide parameter field for molecular communication is scarce and often difficult to generate. In this work, a biocompatible testbed for molecular communication with magnetic nanoparticles is used to investigate a series of transmission channel parameters. The observed results are discussed in the context of a laminar flow channel. All experimental data regarding the parameter studies as well as an additional data set for a large binary transmission sequence is provided as a supplement to this publication. The data is available on a public server to allow for further use by other researchers.
{"title":"Channel Parameter Studies of a Molecular Communication Testbed With Biocompatible Information Carriers: Methods and Data","authors":"Max Bartunik;Janina Teller;Georg Fischer;Jens Kirchner","doi":"10.1109/TMBMC.2023.3325405","DOIUrl":"10.1109/TMBMC.2023.3325405","url":null,"abstract":"Testbeds play an essential role in the development of real-life molecular communication applications and experimental validation of communication channel models. Although some testbed concepts have been published in recent years, very few setups are inherently suitable for biomedical applications. Furthermore, systematic experimental data of a wide parameter field for molecular communication is scarce and often difficult to generate. In this work, a biocompatible testbed for molecular communication with magnetic nanoparticles is used to investigate a series of transmission channel parameters. The observed results are discussed in the context of a laminar flow channel. All experimental data regarding the parameter studies as well as an additional data set for a large binary transmission sequence is provided as a supplement to this publication. The data is available on a public server to allow for further use by other researchers.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"489-498"},"PeriodicalIF":2.2,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135056618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-13DOI: 10.1109/TMBMC.2023.3324487
Mohammad Javad Salariseddigh;Vahid Jamali;Uzi Pereg;Holger Boche;Christian Deppe;Robert Schober
Various applications of molecular communications (MC) are event-triggered, and, as a consequence, the prevalent Shannon capacity may not be the right measure for performance assessment. Thus, in this paper, we motivate and establish the identification capacity as an alternative metric. In particular, we study deterministic identification (DI) for the discrete-time Poisson channel (DTPC), subject to an average and a peak molecule release rate constraint, which serves as a model for MC systems employing molecule counting receivers. It is established that the number of different messages that can be reliably identified for this channel scales as $2^{(nlog n)R}$